Bioorganic & Medicinal Chemistry Letters 24 (2014) 450453

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Bioorganic & Medicinal Chemistry Letters

journal homepage: www.elsevier.com/locate/bmcl

Alkylamino derivatives of pyrazinamide: Synthesis

and antimycobacterial evaluation
Barbora Servusov , Pavla Paterov, Jana Mandkov, Vladimr Kubcek, Radim Kucera, Jir Kune,
Martin Dolezal, Jan Zitko
Faculty of Pharmacy in Hradec Krlov, Charles University in Prague, Heyrovskho 1203, Hradec Krlov 500 05, Czech Republic

a r t i c l e

i n f o

Article history:
Received 1 November 2013
Revised 11 December 2013
Accepted 12 December 2013
Available online 19 December 2013
Keywords:
5-Chloropyrazine-2-carboxamide
6-Chloropyrazine-2-carboxamide
Alkylamines
Antimycobacterial activity
Cytotoxicity

a b s t r a c t
A series of pyrazinamide derivatives with alkylamino substitution was designed, synthesized and tested
for their ability to inhibit the growth of selected mycobacterial, bacterial and fungal strains. The target
structures were prepared from the corresponding 5-chloro (1) or 6-chloropyrazine-2-carboxamide (2)
by nucleophilic substitution of chlorine by various non-aromatic amines (alkylamines). To determine
the inuence of alkyl substitution, corresponding amino derivatives (1a, 2a) and compounds with
phenylalkylamino substitution were prepared. Some of the compounds exerted antimycobacterial activity against Mycobacterium tuberculosis H37Rv signicantly better than standard pyrazinamide and corresponding starting compounds (1 and 2). Basic structureactivity relationships are presented. Only weak
antibacterial and no antifungal activity was detected.
2013 Elsevier Ltd. All rights reserved.

According to the WHO Global Tuberculosis Report 2013 estimates, in 2012 there were 8.6 million new cases of tuberculosis
(TB) and 1.3 million deaths associated with TB.1 Although the absolute number of TB cases per year has been slightly decreasing since
the beginning of millennium (decrease from 144 cases per 100,000
population in 20002 to 125 cases per 100,000 population in 2011,3
TB still remains 2nd leading cause of death from an infectious disease worldwide.1 The situation is worsening due to the co-infection with HIV (1.1 million of all TB cases and 0.32 million of
deaths per HIV-associated TB).1,4 Another serious problem highlighting the need for new antituberculotics is the increasing number of resistant TB-forms, namely multidrug-resistant (MDR) and
extensively drug-resistant (XDR) TB.1,4
5-Chloropyrazine-2-carboxamide (5-Cl-PZA), derived from
rst-line anti-TB drug pyrazinamide (PZA) and originally prepared
by Asai5, proved in vitro antimycobacterial activity against
PZA-sensitive Mycobacterium tuberculosis strains (MIC = 832 lg/
mL) as well as PZA-resistant mycobacterial strains (Mycobacterium
kansasii, M. smegmatis, M. fortuitum, M. avium; MIC = 864 lg/mL).6
However, 5-Cl-PZA was not active in vivo in a chronic murine TB
model7 (probably due to metabolic instability or poor pharmacokinetics). Its mechanism of action results from the inhibition of
fatty acid synthase type I811 (FAS I,12 the crucial enzyme participating in the synthesis of mycolic acids, vital components of
Corresponding authors. Tel.: +420 495067272; fax: +420 495518002.
E-mail addresses: barbora.servusova@faf.cuni.cz (B. Servusov), jan.zitko@faf.
cuni.cz (J. Zitko).
0960-894X/$ - see front matter 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.12.054

mycobacterial cell wall). The specic mechanism seems to be the

competitive displacement of the NADPH cofactor from FAS I.13
For this mechanism of action, carboxamido group does not need
to be metabolized to carboxylic group. Our attention was focused
on substitution of chlorine in 5-Cl-PZA (1) by alkylamines. The positive inuence of long alkyl chains (C6, C7) on antimycobacterial
activity was observed in previous studies on pyrazine derivatives.14,15 Long alkyl chains are not a common part of designed or
therapeutically used drugs. Nevertheless, recently discovered
mycobacterial enoyl-ACP-reductase InhA inhibitors derived from
triclosan contained long alkyl chains in their structure.16,17 As InhA
is located in mitochondria,18 it is obvious that compounds with
long alkyl chains are able to penetrate through mycobacteria outer
shell and cell wall, reaching the intracellular compartments.
To compare relationships between substituents position and
activity, the analogous series derived from 6-chloropyrazine-2carboxamide19 (2, 6-Cl-PZA) was prepared. To study the inuence
of alkyl chain on activity, simple aliphatic chain was replaced by
phenylalkyl chain (compounds 1j, 1k, 2j and 2k). Amino derivatives (1a, 2a) were prepared as well.
This research project presents the series of 22 compounds, their
synthesis, methods and results of biological screening. 5-Cl-PZA
was prepared by convenient two-step synthesis using 5-hydroxypyrazine-2-carboxylic acid (Sigma Aldrich), which was treated
with thionyl chloride to form 5-chloropyrazine-2-carbonyl
chloride,20 see Scheme 1. The subsequent aminolysis by 25% aq
ammonia afforded 5-Cl-PZA as a precipitate, which was separated
by ltration. The formation of acyl chloride was catalyzed by

B. Servusov et al. / Bioorg. Med. Chem. Lett. 24 (2014) 450453

451

Scheme 1. Synthesis of starting compounds 1 and 2.

N,N-dimethylformamide (DMF).21 Synthesis of 6-Cl-PZA was carried out analogously from 6-chloropyrazine-2-carboxylic acid22
obtained from pyrazine-carboxylic acid via N-oxide23 and its subsequent chlorination with phosphoryl chloride.24 Final structures
were prepared from chloro-pyrazinamide (1 or 2) by means of
nucleophilic substitution of chlorine by aliphatic alkylamines or
phenylalkyl amines, see Scheme 2. Different approach was applied
for the synthesis of amino compounds 1a25 and 2a,26 where the
microwave irradiation was used to accelerate the aminodehalogenation reaction (described in Supplementary data). Synthesis
and antimycobacterial activity of 6-methylaminopyrazine-2carboxamide (2b) was previously published by Foks and
co-workers27 (added to Table 1 for clarity).
All compounds (including standards PZA, INH and starting
compounds 5-Cl-PZA = 1 and 6-Cl-PZA = 2) were screened for
antimycobacterial activity against four mycobacterial strains
(Mycobacterium tuberculosis H37Rv, M. kansasii 235/80, M. avium
80/72 and M. avium 152/73) by microplate alamar blue assay
(MABA)28 at pH = 5.6 (conditions optimized for PZA).29 Results
were expressed as minimal inhibitory concentration (MIC) in
lg/mL, data in parentheses represent the MIC values with respect
to molecular weight in lM (Table 1). The MIC values for 5-Cl-PZA
(1, MIC = 50 lg/mL) were approximately in accordance with
previously published data (MIC = 832 lg/mL).6
In the presented series, the substitution of chlorine with long
alkylamine chain (heptyl, octyl) led to a signicant increase in antimycobacterial activity and thereby also conrmed the previously
reported positive inuence14,15 of long alkyl chains on antimycobacterial activity. Besides increased lipophilicity, this effect might also
be mediated by facilitated transport through mycobacterial cell
wall, via interaction of long carbon chains of mycolic acids with alkyl
chains of discussed compounds. Taking into account molecular
weight (MIC values converted to molar concentration lM), 6-octylaminopyrazine-2-carboxamide (2i, MIC = 6 lM) was signicantly
more active (up to 100-fold) against M. tuberculosis H37Rv than
corresponding starting compound 6-Cl-PZA (2, MIC = 635 lM), see
Table 1. This compound 2i also exhibited activity against all
PZA-resistant strains (MIC = 25 lg/mL i.e. 100 lM).
In the series derived from 5-Cl-PZA (1), heptylamino (1h,
MIC = 53 lM) and octylamino (1i, MIC = 25 lM) derivatives also

Scheme 2. Synthesis of nal compounds 1ak and 2ak. Reagents and conditions:
alkylamines (in the range from methyl to octylamine) or phenyl alkylamines were
reuxed in EtOH for 6 h; 1a, 2a: 25% aq ammonia, MW.

exhibited signicant increase in activity against M. tuberculosis

H37Rv compared to starting compound 1 (MIC = 317 lM). Remarkably, the activity of 1h (MIC = 53 lM) and 1i (MIC = 25 lM) against
M. kansassi was slightly better than activity of 5-Cl-PZA (1,
MIC = 79 lM). Within all compounds, the activity of octylamino
derivatives (MIC = 6-25 lM) against M. tuberculosis H37Rv was signicantly higher comparing to the activity of therapeutically used
PZA (MIC = 102205 lM).
Insertion of aromatic nucleus into the aliphatic chain (1j, 1k, 2j
and 2k) led either to decrease or complete loss of activity. Derivatives with amino substitution or with shorter alkylamino chain
(methyl to pentylamino subst.) were completely inactive against
all tested strains. Lack of activity of compounds 1af and 2af
could be possibly caused by low lipophilicity and/or poor ability
to penetrate lipophilic mycobacterial cell wall. Except for
compounds with phenylalkylamino substitution (1j, 1k, 2j, 2k),
no signicant differences in activity were observed between
5-alkylamino series and their 6-alkylamino isomers.
Lipophilicity is an important (but not the only) determinant of
antimycobacterial activity in presented homologous series. Steric
effects, possible interactions of amino moiety as well as exibility
of alkyl chain play important role. However, some dependence of
antimycobacterial activity on lipophilicity can be observed.
Graph 1 reveals signicant correlation (r = 0.8558; P = 0.0016;
R2 = 0.7323; n = 10) of antimycobacterial activity expressed as log
(1/MIC) in molar concentration on lipophilicity (log k) for
compounds with detected MIC.
As seen from Graph 1, most of the compounds with signicant
antimycobacterial activity (MIC 6 25 lg/mL) had lipophilicity
log k P 0.3. In our system this value corresponds approximately
to C log P about 3.0. For the sake of completeness, values for
5-Cl-PZA (1) and 6-Cl-PZA (2) were added to the graph.
In vitro hepatotoxicity assay was performed for compounds with
MIC 612.5 lg/mL (1h, 1i and 2i), PZA and starting compounds 1 and
2. The decrease of viability of human liver HepG2 cells was measured using standard colorimetric assay based on the reduction of
tetrazolium.30,31 Results were expressed as IC50. The course of the
toxicity curves of PZA, 1h and 1i did not allow a valid calculation
of IC50 due to the limited solubility in the cell culture medium. Thus,
only an estimate of toxic concentrations could be determined for
these compounds. According to HepG2 cytotoxicity, the studied
compounds can be divided in two groups. The rst group includes
compound 2i having intermediate toxicity in HepG2 cells. The
second group is formed by relatively in vitro non-toxic compounds
1, 2 and PZA as well as 1h and 1i, see Table 2. Selectivity index (SI)
dened as IC50/MIC in molar concentrations was calculated for antimycobacterial activity against M. tuberculosis.
SI values over 10 are considered as safe for a drug candidate,
granting the sufcient difference between efcient and cytotoxic
concentrations. Compounds with octylamino substitution (1i and
2i) possessed SI > 10. The difference between cytotoxicity of
5-Cl-PZA (1) and 6-Cl-PZA (2) could be caused by altered

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B. Servusov et al. / Bioorg. Med. Chem. Lett. 24 (2014) 450453

Table 1
Summary of prepared compounds. Their antimycobacterial activity (detected at pH = 5.6) expressed as minimal inhibition concentration (MIC) in lg/mL or with respect to
molecular weight of compounds in lM. Comparison of calculated lipophilicity parameter (C log P) with determined log k values.
Antimycobacterial activity (lg/mL) (lM)

Structure
No.

1a
H
1b
Methyl
1c
Ethyl
1d
Propyl
1e
Butyl
1f
Pentyl
1g
Hexyl
1h
Heptyl
1i
Octyl
1j
2-Phenylethyl
1k
3-Phenylpropyl
2a
H
2b
Methyl
2c
Ethyl
2d
Propyl
2e
Butyl
2f
Pentyl
2g
Hexyl
2h
Heptyl
2i
Octyl
2j
2-Phenylethyl
2k
3-Phenylpropyl
1 = 5-Cl-PZA
2 = 6-Cl-PZA
PZA
INH

MW

M. tbc H37Rva

M. kansasiib

M. avium

138.13
152.15
166.18
180.21
194.23
208.26
222.29
236.31
250.34
242.28
256.30
138.13
152.15
166.18
180.21
194.23
208.26
222.29
236.31
250.34
242.28
256.30
157.56
157.56
123.11
137.14

>100
>100
>100
>100
>100
>100
50 (225)
12.5 (53)
6.25 (25)
50 (206)
25 (98)
>100
n.a.
>100
>100
100
100
100
25 (106)
1.56 (6)
>100
>100
50 (317)
100 (635)
12.525 (102205)
0.391.56 (311)

>100
>100
>100
>100
>100
>100
100
12.5 (53)
6.25 (25)
100
100
>100
n.a.
>100
>100
>100
>100
>100
50 (212)
25 (100)
>100
>100
12.5 (79)
>100
>100
1.566.25 (1146)

>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
n.a.
>100
>100
>100
>100
>100
100
25 (100)
>100
>100
>100
>100
>100
12.5

Lipophilicity
c

M. avium

>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
>100
n.a.
>100
>100
>100
>100
>100
100
25 (100)
>100
>100
>100
>100
>100
6.25

log k

C log P

0.7852
0.6878
0.5520
0.3878
0.1910
0.0181
0.2389
0.4658
0.6930
0.0382
0.1408
0.7814
n.d.
0.6318
0.4386
0.2162
0.0095
0.2051
0.4273
0.6514
0.0986
0.0741
0.3891
0.4165
0.6872
0.7432

0.6797
0.1466
0.6756
1.2046
1.7336
2.2626
2.7916
3.3206
3.8496
2.2436
2.6226
0.6797
0.1466
0.6756
1.2046
1.7336
2.2626
2.7916
3.3206
3.8496
2.2436
2.6226
0.0613
0.0613
0.6763
0.6680

Numbers in parentheses represent the MIC values converted to molar concentrations (lM) n.a. data not available n.d. not determined.
CNCTC = Czech National Collection of Type Cultures.
a
CNCTC My 331/88.
b
CNCTC My 235/80.
c
CNCTC My 80/72.
d
CNCTC My 152/73.

Table 2
Cytotoxicity of selected compounds in HepG2 cells
No.

1h
1i
2i
1 = 5-Cl-PZA
2 = 6-Cl-PZA
PZAa

HepG2

M. tbc H37Rv

IC50 (lM)

SI

MIC (lg/mL)

MIC (lM)

>250*
>250*
161
1.6  103
3.5  103
>1  104*

>4.7
>10.0
25.8
5.0
5.5
>98.1

12.5
6.25
1.56
50
100
12.5

53
25
6
317
635
102

Testing in higher concentration was limited due to the solubility of the tested
compounds.
a
PZA IC50 = 79.1 mM, data from literature.32

Graph 1. Correlation of antimycobacterial activity on experimentally measured log

k values. Inactive compounds, for which no exact value of MIC was detected
(MIC > 100 lg/mL), were omitted. 5-Cl-PZA and 6-Cl-PZA were not included in the
correlation. The striped region represents desired lipophilicity values with respect
to activity. Correlation parameters: r = 0.8558; P = 0.0016; R2 = 0.7323; n = 10.

biodegradation. PZA derivatives are metabolized via xanthine oxidase and aldehyde oxidase to form 5-hydroxy derivatives.33 We
might hypothesize that 5-chloro substitution interferes with the
hydroxylation process.
For all tested compounds and strains, only weak antibacterial
activity was found for compound 2g (Staphylococcus epidermidis
H 6966/08; MIC = 62.5 lM), for further details see Supplementary
data. The rest of tested compounds were inactive even in highest
concentrations used in the testing, which were 500 lM.

Concerning the mechanism of action, PZA acts mainly as a

prodrug, which is enzymatically hydrolysed via mycobacterial pyrazinamidase (PncA, EC 3.5.1.19) to form pyrazinoic acid (POA).34
On the other hand, some PZA derivatives proved to be active in
non-hydrolysed carboxamide form; for example, 5-Cl-PZA as a
FAS I inhibitor.6,8,9,11,13 5-Cl-PZA possessed in vitro activity against
mycobacterial strains with low pyrazinamidase activity as well.7
To elucidate, whether the most active alkylamino derivatives of
PZA could underwent hydrolysis by PncA or rather function in
non-hydrolysed form, a docking study was performed.
Crystallographic structure of PncA was recently described in
detail.35 The substrate binding cavity in PncA is a narrow crevice
(approximately 10  7 ) containing catalytic triad made of residues Lys96, Asp8 and Cys138. On the opposite site of the crevice,
three histidine residues (His51, His57 and His71) and Asp49 hold
the Fe ion on. According to the orientation of PZA needed for its
catalytic conversion as described in literature,35 the substituents

B. Servusov et al. / Bioorg. Med. Chem. Lett. 24 (2014) 450453

on C5 and C6 of the pyrazine nucleus would protrude towards the

end of the cavity formed by the Trp68. The distance between the
PZA ring and the Trp68 plane is approximately 45 (see Supplementary data), which is little space to accommodate any larger
substituent. Therefore, we expected that the 5-alkylamino and
6-alkylaminopyrazine-2-carboxamides with longer alkyl chains
would have to be displaced from the position needed for the
catalytic transformation. This was conrmed by docking study
described in Supplementary data. To conclude, neither 5-alkylamino nor 6-alkylamino derivatives of PZA will be converted to
corresponding carboxylic acids by the PncA.
New series of 5-alkylamino and 6-alkylaminopyrazine-2carboxamides were synthesized, characterized by analytical data
and screened for antimycobacterial activity. 6-Octylamino-pyrazine-2-carboxamide (2i) showed the highest activity against M.
tuberculosis H37Rv (MIC = 1.56 lg/mL i.e. 6 lM), broadest
spectrum of activity as well as highest selectivity index for M.
tuberculosis H37Rv (SI = 25.8) within all compounds. Based on the
results, we presume 6-octylaminopyrazine-2-carboxamide (2i,
100-fold more active than 6-Cl-PZA) could serve as model structure for further modications. Presented study also conrmed
the previously reported positive inuence of long alkylamino
chains on antimycobacterial activity.
Acknowledgments
This work was nancially supported by GAUK B-CH/710312,
IGA NT 13346 (2012) and SVV-2013-267-001. The publication is
co-nanced by the European Social Fund and the state budget of
the Czech Republic. Project no. CZ.1.07/2.3.00/20.0235, the title
of the project: TEAB.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2013.12.
054.
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